No logistically and functionally it doesn't make sense for them to have two sets of ears. From a biological stand point assuming faunus evolved from humans it makes perfect sense. There are dozens of different traits in your body that don't actually have a purpose, they're left over pieces of an earlier evolution of humanity and in five or six generations they will eventually get edited out.

The same is true of other mammals, many of them have traits both internal and external that serve no purpose and in some cases are actually detrimental. Evolution is a very slow process that takes a great deal of time. It's not going to be suddenly an entire generation of faunus don't have regular human ears. It's going to be that the human ears slowly disappear over a couple hundred or even thousand years.